An invisible workforce in soil: The neglected role of soil biofilms in conjugative transfer of antibiotic resistance genes

Abstract

Soil, a potential reservoir of antibiotic resistance genes (ARGs), is inhabited by numerous microorganisms. Many microorganisms in soil are embedded within a self-produced matrix of extracellular polymeric substances to form supracellular structures, i.e., biofilms. Representing the predominant microbial lifestyle in soil, soil biofilms are considered hot spots of horizontal gene transfer. Herein, we discuss the distribution, transfer, and fate of ARGs in the soil environment at macro- and micro-scales. Applications of microfluidic platforms, with an advantage of mimicking complex soil environments and permitting the study of microbial behaviors at a micro-scale, coupled with high-throughput sequencing and other innovative platforms, to study soil biofilms and transfer of ARGs are also discussed. This review aims to highlight the neglected role of soil biofilms in the spread of ARGs to expand the current limited knowledge about ARGs in the soil microenvironment.

Graphical abstract

Keywords:

• Soil microbiome
• soil biofilms
• antibiotic resistance genes
• conjugative transfer
• microenvironments
• microfluidic technique

Disclosure statement

The authors declare no competing financial interest.

Additional information

Funding

This work was supported by the National Natural Science Foundation of China (41877029, 41961130383), Royal Society-Newton Advanced Fellowship (NAF\R1\191017), and Wuhan Science and Technology Bureau (2019020701011469).